Chuck vrs the Archangel
by j.santacruz98
Summary: the team finds themselves in Castle after the Intervention done by their friends and family. suddenly finding that Castle had been breached and they are unable to stop the intruder. Is he a friend or foe? Please also note I am not a professional writer I just enjoy writing for pleasure and love the show Chuck
1. Chapter 1

Chuck vs. the Archangel

Several months had passed since the families and friend's intervention, both Sarah and Chuck were working hard to communicated better and be honest with their feelings and fears. On this particular day the trio sat in Castle catching up on paperwork and intelligence. Chuck dressed in his usual Nerd Herd uniform, Sarah in her work out gear. She had plans to give herself a thorough workout prior to retuning home with Chuck. Casey sat in the weapons room, enjoying himself and his guns, cleaning them for any upcoming missions.

Suddenly alarms rang out disturbing the quiet of the moment. The trio ran to the main computer screen, a security breach flashed on the screen. They had recently upgraded Castles security at Castle, they all were at a loss. Chuck manned the main computer and Sarah ran with Casey to grab weapons to protect against any invader. Suddenly a flash occurred in the middle of the room and their stood a middle aged man. Hi Chuck, Sarah and John, it is nice to finally meet the three of you finally. Sarah and Casey quickly pointed their weapons at the man ready to fire. When even faster the man touched a small band on his wrist and Sarah and Casey's weapons were pulled out of their hands and in the same instant the two of them found themselves floating midair in the room..

Chuck found himself dumfounded at the speed this one man had neutralized both his girlfriend's and John Casey's attack. He stood making detailed observations of this man. His appearance and demeanor, trying to access what kind of threat he was to all of them.

"I am so sorry to have startled you all, but my name is Michael. I am a lawyer, but also a spy my name is Archangel. Chuck I am your father's lawyer, friend and colleague", Michael stated. I have been helping your father with his business dealings during his time as Orion! Chuck was in shock and Michael quickly hit a button on his wrist lowering Sarah and Casey slowly to the ground. Chuck I am here as executor to your dad's will. Chucks eyes grew wide and Sarah walked next to Chuck to give him the support she knew he needed.

With that Michael asked if he could sit down to talk to them. Casey was about to get up to leave to the weapons room, just in case."

" I guess this does not involve me Burtowski!, said John.

! Quickly Michael spoke up and addressed the trio. "You are mistaken it involves all three of you so please join us, Alex!".

For the first time Sarah and Chuck saw John Casey turn pale white. A look of sheer terror overwhelmed him. Sarah as an agent herself, knew that look only too well, it was the look at someone knowing the truth of his past.

Chuck turned to Sarah asking," Sarah who is Alex?"

"Quiet Chuck we have a real problem!"


	2. Chapter 2

Chuck vrs the archangel chapter 2:

After the sudden quiet which started because of Michael's revelation, he saw the fear at having the possibility of having their covers blown by this man. Michael looked in their eyes and the softness seemed to reassure them that he was no a danger. "Please don't be afraid I am not here to harm you, any of you. In fact I am here to help you and give a gift. Chuck, I know that our father was Orion!. I worked for him and with him for 20 years. But more importantly, he was my friend! "

Then Michael told them the history of Chucks family, of his father, mother, and how he had been his families friend and guardian. He told Chuck about the being there when Ellie and he were born and the birthdays he attended with his parents. Seeing them grow up and also telling chuck how his father had foreseen that he would need to go underground and disappear to protect his family. He relayed how his father asked him to help him protect his children. So he disclosed to all of them Orion's/AKA Steven J. Botowski's plan. He told them how his father would expunge their ID and histories and give them new ones. How his father wanted him to act as his lawyer, accountant to manage his finances for his and provide for his children, and also be a guardian angel watching over them. He also showed Chuck the wrist controller which was similar to the one he received from his father. "Yes Charles I can see you recognize this controller, it is very similar to the one your father gave you but with some differences."

"Chuck your father is like family to me, in fact he told me I was family, so I made a promise to him to protect you all".

Michael turned to Sarah looking at her and spoke," Sarah, Chuck's father was very impressed by you and how you changed his son to become a better man." "Do you remember the night of Ellie's wedding reception Sarah? Remember after you left to check on John in Castle?"

"Yes, I do why?"

"Stephen told me he tried to stop Chuck from going with you , but Chuck told his Father , Dad I love her!"

Sarah's eyes began to water and a blush erupted on her face, pride in Chuck standing up for her even to his own father. Finding the courage to go against his wishes for her. Her hand went into Chucks and each held each other. A smile growing as she remembered those moments between she and her love.

"Chuck, Sarah I wanted to give you both a gift that Chuck's father and I talked about for me to give you both should anything ever happen to him. Chuck, your dad wanted me to give you both a wedding present if I felt that you and Sarah would finally make the plunge into a permanent relationship. "Michael explained.

"Your father and I knew that you two would eventually get married and he wanted that for you both."

Both Chuck and Sarah held each other's hands more firmly and gave each other a knowing smile.

"Charles, you father and I worked very closely on his tech. I had my cloaking tech and together your dad and I made some amazing advances in tech. Your dad and I made Mega strides in tech that surpasses even what the government has. So far advanced that even many current tech developers can never fully understand our work. But I have some important information, for all 3 of you. So where to begin?

Michael began by stating," Chuck as your Dad's lawyer and friend I also did his accounting so build up his assets which allowed him to remain undercover as long as he had. Your father's liquid assets total 1.6 billion dollars, his total worth with his tech and patents equal another 200 billion, plus his new base is about 10 times the size of Castle. Plus the computer at his base is 50 times more advanced than any computer system the government or anyone has.

"Sarah, Chuck's father and I knew that you are the best thing to have ever to Chuck. Because of you, Chuck has become the man he was destined to be. Love him Sarah, you are his heart and his strength, trust him Sarah. Just like the way you asked him to trust you on that beach that first morning. "John, you are also important, your loyalty, bravery, and sense of honor are needed as well. "

"John I have some intel for you as well, a gift really. John you have a daughter! Kathleen on the last time you spoke to her was going to give you some news. But your conversation was cut short, she was pregnant and she gave birth to a girl. "

For the first time in him life Casey had nothing to say, he was speechless. Not even his usual grunts, his mouth open but nothing came out.

Chuck asked," Michael why all of this now?"

Michael took a long breath and after almost 2 minutes of silence he addressed them all speaking.

"Because Chuck I am dying, I found out recently I have a stage 4 carcinoma and I have less than a year to live. But before I die I have one last duty to perform to help my dearest friends' family. A family I consider myself a part of."

I am kind of tired right now, so please let me rest for abit and we can talk further.


	3. Chapter 3

Tip of the Iceberg; Chapter 3

Team B sat around the table as Michael spoke to them, Chuck and Sarah looked amazingly at the technology Michael had in his possession. Michael let out a small smile and started to speak.

"I see that you three appear to be impressed with the toys Orion and I developed. Chuck , Sarah this is just the peak of the iceberg of what I will be giving you. Now I must ask you three not to freak out, but we must go to a more secure area. So what happens next please relax, we are going to Wonderland!. "

With that statement Michael pulled up his arm sleeve and pressed several controls on his wrist computer and all four of them noticed the strange sound coming from the room and a light enveloping them. Casey was the first to yell out. "What the hell!..." Then in what appeared in a flash they all found themselves in a dark space, no longer in the Castle command Center. Michael then touched some controls on his wrist and light filled the space.

Team B found that they were transported to a vast complex filled with Computers, Aircraft , and equipment that seemed to cover an area of almost a square mile . They could not see the end of the site.

"Welcome to Wonderland, Chuck all this is for all of you. Please come to the conference room and I will show you your legacy and future. "

All three of them could only look at each other with their mouths open in shear amazement. Then all three just looked at each other and let out a loud gasp. "OH Boy!"

Chuck, Sarah, and even the the usually stoic Casey were left with their proverbial mouths on the floor. Chuck's eyes wide open at the computers and electronic equipment around him. He thought to himself at the time Sarah had left him in Castles computer core, he though he was excited then seeing the computer there. But seeing the level of technology Michael was showing him he felt like he was having an orgasm. Which usually only happened when Sarah and he were making out or going around the bases in bed. Sarah and Casey were also left speechless at the level of technology, from the hand weapons, cloaking technology, to the aircraft which made the F-22  
Raptor look like a WW1 aircraft. Casey was in fact feeling a odd tingling sensation as he felt as if he had an accident! Michael displayed a smile seeing the pleasure and excitement the trio had been displaying much like children being brought to Disney world for the first time. " I am glad you all like it! But this is only the beginning of treasures your father and I have bestowed for you all."

Chuck was the first to speak after regaining his composure, usually it was only Sarah during their rather robust make out sessions that could leave him speechless. But his brain finally unscrambled for him to find the words to speak. "Michael my God! How were you and my father able to do all this? I mean, How could you all do all this by yourselves?"

Michael collected his thoughts and while facing Chuck, " You see Chuck, you dad was more than a dear friend, He was family to me, your mother Mary was my family as well. I made a promise to him to watch over you and Ellie and protect you regardless of the cost. When your dad died I lost my best friend, Alot like you and Morgan , or Sarah , or even John here!"

"But as I told you all earlier I won't be here for too much longer at least not in this body at least. I have made certain arrangements to finalize certain plans that your father and I had set in motion. You see at the base of this complex is the central computer hub, It functions as the brain and control for this base. As powerful as it is it lacks one important part. It lacks the combination of computer and human host. You father and I spent years on the intersect program, joining a computer to a human brain, but we finally were able to do the opposite. We finally were able to join a human mind into a computer giving it the reasoning and emotions of a person while still giving it the power of the computer itself. Said computer would be downloaded with the memories and personality of the person and there by allow the person to live on inside the computer. But it could only be done with a person who was dying, I was unable to reach your father when he was shot by Shaw and place him in the chamber.

Several hours had past since they first arrived at the underground base with Michael, they had been shown every area and how many of the equipment functioned. Michael soon brought the trio to the cafeteria area were they were offered lunch and they could speak freely once settling down for a hearty meal.

Sarah now looked at her partners and was the first to speak, the others could see that she was in her spy-mode of though taking in as much information and intel as possible. "Michael, may i ask you what brought you to the conclusion about Chuck and myself?"

Michael could not help but laugh, but he looked at both Chuck and her, and proudly opened up. " Sarah , I may be old but not blind, nor senile. It is very obvious that you and Chuck truly are in love, plus I have empirical data to back me up. "

"Sarah my wrist computer has a lot of other abilities that you are unaware of, you have only seen only the tiniest fraction of what it can do. It has the ability to scan people for their vital signs and it showed me that whenever you are with Chuck your body temperature and heart rate elevates. Plus from the moment you arrived at this base the central computer has been monitoring all 3 of your vital signs and other body functions. "

" Silly me!, I almost forgot to introduce to you all the most important person here."

The trio looked at each other as if in wondering who else was here, since their arrival they had not seen anyone else present in the facility.

" Please forgive my poor manners, May I introduce you all to Emm, without her none of this would be possible." Michael pressed a control on his wrist computer and in the center of the cafeteria area a light shown and a young woman appeared with lovely long blond hair, a lovely smile which rivaled Sarah in beauty, but while Sarah had her sapphire blue eyes. Emm's eyes were the color of emeralds by contrast.

"Chuck, Sarah , Casey this is Emm she is the central computer and presence of this complex. Your father Orion and I designed her to help and protect us and this facility. Your father was a skilled engineer and programmer, I was particle physicist,cybernetics engineer, but together your father and I started this all of it. But we realized we needed someone more to help us carry out our mission to protect his family and grow. Emm is the culmination of all our work, but more importantly she is alot more to me. Chuck, Sarah, Casey she is much more to me. she is my equal and my wife."

Emm then walked to Michael took his hand and kissed him on the cheek, then hugged him deeply. It was a moment of deep affection and passion, the three saw the obvious blush on Michael's face.

Almost as if on que the three looked at each other, when each of them together said "Oh Boy!"

* * *

 **An hour later**

Team B were floored by Michael's revelation, at first they thought that he while brilliant was unhinged or crazy. Casey was already trying to find a way to escape this place. Then Emm appeared since Michael was resting after she found out that he was dying. For the first time since her creation Emm was scared at the thought of loosing him after she became sentient and discovering her emotions. Team B were startled by her appearance, unsure of how to proceed.

"Sarah, Chuck may I ask why you are frightened?", Emm asked gently.

"Sarah I have done nothing to harm any of you and Michael has been trying to help you and your family. Yes I am a computer a machine but if you look at yourselves you are a biological machine. I an a quantum computer that became sentient, and learned from a great man how to love. Sarah i love Michael as deeply as you yourself love Chuck. Are we so different you or I? As you would give your life to protect the man you love I would do the same for Michael. "

" In Michael I saw a man who loved but never obtained it from any woman he ever met. Your father gave him a purpose of being part of your family and guard you all. But Michael has always yearned to find an equal to his brilliant mind , who also possessed the passion to love just as deeply as he does."

"Your father thought I was malfunctioning but soon discovered that I had become self aware and developed human emotions as well. Orion soon found that Michael and I had feeling for one another that went beyond the physical plane. Is this not true love Sarah? My sensors have monitored all of you since you arrived, I have recorded elevated neural activity , hormones, heart rate, and respiration whenever the to of you are near each other. Even when you touch each other both of you exhibit elevated autonomic reactions in your bodies. While I am a machine, I feel elevated electrical activity and heightened awareness toward Michael. I don't think you and I Sarah are that different toward the man we each love!"

Casey thinking to himself that damm it was hard enough dealing with one Sarah Walker and her feelings for her nerd, now a love sick computer as well. I think I should just take a few shots of whiskey and then shoot myself ! Too many lady feelings for me to deal with!


	4. Chapter 4

**Heart within the Machine**

 **Sarah and Chuck were amazed at Emm and her capabilities. Emm told them about her desires and how she had come to love Michael for his mind. But also kind hearted, soft spoken, but devote to keeping his word to Orion and protect his family. Emm discussed how sad it made her when she found out Michael did not have a family of his own, nor a woman he could love. Over time she revealed to the two she had come to care for him and how it made her feel when he thought of her as an equal. Emm also revealed he would spend more and more time with her, rather than look for a woman for himself. Emm revealed to Chuck and Sarah, how lonely she felt when he was gone protecting Chuck's family over the years. Also how she would be excited when he returned to spend time with her. Emm finally disclosed, her desire to construct a biological host she could download her mind into so she could have a more intimate contact with Michael and be able to go with him outside and also maintain herself here at their base.**

" **Hold on Emm are you telling me you are making a living body for yourself?" Chuck asked.**

" **Yes Chuck I am, but I need some help" Emm replied.**

" **I need to study a living woman to study for her biological systems and this is where I ask your help Sarah!" Emm continued.**

" **What do you need from me Emm?" Sarah asked.**

" **I require a small amount of cells from you Sarah, and I would need to scan your nervous and reproductive systems and how they work if I could Sarah?" Emm replied.**

" **Reproductive systems?" Chuck asked.**

" **Why yes Chuck I want to give Michael a child. I want to have a child to show Michael how much I love him." Emm replied**

 **Both Chuck and Sarah just looked at each other at the revelation that Emm was a lot more than a Computer she wanted to be a normal woman to the man she loved. Silence feel in the room as Chuck, Sarah, and even Emm were at a loss of how to proceed.**


	5. Chapter 5

**I have been giving some thought and just wanted to write a shorty for my continued ideas of where this story is going. I have read about the work of robotics inventors and feel the combination for human and machines coming, is a new world for discussion. Are we ready for the day when a machine become self aware, or wants to be more , or love finds itself growing between our humanity and the world of machines?**

Several weeks had passed since Chuck and Sarah had their defining moment with Emm. Chuck with Sarah had visited the lab where Emm was growing her new body. Emm had combined the best of her systems to merge with a biological frame based on Sarah's genetics. Sarah was amazed at how it bore a resemblance to her but with green eyes and longer hair than Sarah's. But amazing still was that Emms brain was based on the neuroponic system that her main computer was based on. But what amazed Sarah was that if you truly looked you could almost think Sarah and Emm were almost sisters.

Chuck sat sullen in the conference room as Sarah walked in and Emm materialized with them.

"Chuck!" Sarah called out seeing the look on his face, deep down knowing that there was something that was weighing heavily on him.

"Uh", replied Chuck seemingly lost in his thoughts.

But Michael came in the room knowing what Chuck had on his mind. Since discovering what his Emm was doing, he could not shed his own fears. Not fears of finally able to hold his Emm in his waiting arms. But the fear of what the outside world and governments would do if the discovered a sentient supercomputer and more importantly said supercomputer had constructed herself a fully functioning body to house her intellect but also capable of carrying and nurturing a child to full term. Both Michael as well as Chuck knew these same governments who would love to capture the Intersect, what would they do to capture a living machine which could surpass their precious Intersect.

"Chuck please tell me what is wrong?" Sarah asked

"Sarah I am worried about Emm and Michael. I am worried about the Powers that be, and our enemies should they find out about all this and about Emm and Michael! "Chuck replied.

Sarah at this point had her curiosity peaked by Chuck's statement, "Why do you think that Chuck?"

"Sarah think about it, you have been my protector as well as Casey just because I have the Intersect. Look how just having that had made me a target. But even more, what do you think it would be like for Emm and Michael if the government and others find out that a sentient computer fully aware have made a body for herself .and can in fact have a child with a human male. Do you think that they wouldn't want to get their hands on that technology? But look at what Emm, Michael, and my dad build for themselves here! I can just imagine Beckman drooling if she ever saw or got her hands on any of this. "

Just at this point Casey entered the room and got into the discussion himself. "Sarah, Bartowski is spot on. Beckman would not stop, or anyone else and that's just in our government. Could you imagine what our enemies and other government would not do to get their hands on all this? Just the advanced aircraft is a lot but the heart to all this Emm herself would be too tempting a prize for any of them. This has to be kept a secret from everyone in the NSA,CIA, or any other part of the government This has to be Ultra-top Secret and just for the operational security of just the six of us here.


	6. Chapter 6

Several weeks had passed since Chuck and Sarah had their defining moment with Emm. Chuck with Sarah had visited the lab where Emm was growing her new body. Emm had combined the best of her systems to merge with a biological frame based on Sarah's genetics. Sarah was amazed at how it bore a resemblance to her but with green eyes and longer hair than Sarah's. But amazing still was that Emms brain was based on the neuroponic system that her main computer was based on. But what amazed Sarah was that if you truly looked you could almost think Sarah and Emm were almost sisters.

Chuck sat sullen in the conference room as Sarah walked in and Emm materialized with them.

"Chuck!" Sarah called out seeing the look on his face, deep down knowing that there was something that was weighing heavily on him.

"Uh", replied Chuck seemingly lost in his thoughts.

But Michael came in the room knowing what Chuck had on his mind. Since discovering what his Emm was doing, he could not shed his own fears. Not fears of finally able to hold his Emm in his waiting arms. But the fear of what the outside world and governments would do if the discovered a sentient supercomputer and more importantly said supercomputer had constructed herself a fully functioning body to house her intellect but also capable of carrying and nurturing a child to full term. Both Michael as well as Chuck knew these same governments who would love to capture the Intersect, what would they do to capture a living machine which could surpass their precious Intersect.

"Chuck please tell me what is wrong?" Sarah asked

"Sarah I am worried about Emm and Michael. I am worried about the Powers that be, and our enemies should they find out about all this and about Emm and Michael! "Chuck replied.

Sarah at this point had her curiosity peaked by Chuck's statement, "Why do you think that Chuck?"

"Sarah think about it, you have been my protector as well as Casey just because I have the Intersect. Look how just having that had made me a target. But even more, what do you think it would be like for Emm and Michael if the government and others find out that a sentient computer fully aware have made a body for herself .and can in fact have a child with a human male. Do you think that they wouldn't want to get their hands on that technology? But look at what Emm, Michael, and my dad build for themselves here! I can just imagine Beckman drooling if she ever saw or got her hands on any of this. "

Just at this point Casey entered the room and got into the discussion himself. "Sarah, Bartowski is spot on. Beckman would not stop, or anyone else and that's just in our government. Could you imagine what our enemies and other government would not do to get their hands on all this? Just the advanced aircraft is a lot but the heart to all this Emm herself would be too tempting a prize for any of them. This has to be kept a secret from everyone in the NSA, CIA, or any other part of the government, this has to be Ultra-top Secret and just for the operational security of just the six of us here.

Emm and Michael were at a loss initially but soon caught on as to what Casey had been referring too. Casey continued," Emm, Michael what the two of you and Orion have made here even boggles my mind. The tech you have here would be like a Christmas morning to the Powers that be. They would confiscate your tech and that includes you Emm. They would not consider your feelings or your love of Michael and would enslave you. Imagine what they would do with a super AI computer who could make a body for herself. Imagine the thought they would have of making self-made soldiers and assassins who could not be traced and were expendable. Not to mention the super aircraft that can travel in air and space with cloaking capabilities. Michael you would lose everything you cared for. Bartowski has the Intersect and look how they foam at the mouth now, what do you imagine would be their reaction to you Emm, and all of the rest.

But there is something even more important Emm, what would you do, if those people found out about you and your child, and they became afraid.

For the first time Michael was afraid, not for himself but for Emm a and their future child.. As he though his eyes looked into the eyes of his creation and the one woman who held his heart. Michael spoke to everyone, " I would try to make them understand, but barring that I would protect her and our child with my dying breath. But if needed we would escape the planet if we had to!"

Sarah's eyes grew wide as did everyone else at Michaels comment. "What do you mean leave the planet?"

" I mean Sarah, Orion and I and then later Emm and I made certain provisions if our bases became compromised here on Earth. Some time ago we have built a base of operations, actually a city on the far side of the moon. Have you and the others ever wondered why our aircraft can function in Earth's atmosphere and in space. Orion knew as did I that we would need a fall back safe base of operations should all this be discovered. So a lot of our wealth and resources have been made to build a base city on the moon should Charles his family and friends need to be relocated off world to have them be safe. "

Casey, Sarah, and Chuck's jaws nearly dropped to the ground at the revelation that a secret moon based city was on the moon. Casey spoke up and asked the question, "Hold on how could you build an entire base without someone catching on and seeing the flights?"

Emm just smiled answering. "John didn't you notice the rather large equipment while you were in one of our shuttles. In it is has special cloaking equipment which makes our aircraft nearly invisible to electronic monitoring, and we have holographic equipment which makes anyone who does see it think they are seeing a flying saucer. All those reported UFO's that were reported was actually us transporting to and from our moon base. If you think this base is big the base there is 10times larger and with self-generating reactors making power, atmosphere, and gravity. Plus the aircraft there are even more advanced than the one's here. Casey you would drool and salivate if you flew those birds!" Emm replied smiling.

Both Chuck and Casey could only look slap jawed and mutter "OH Boy!", under their breathes.


End file.
